+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2854 | |||||||||
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Title | CryoEM structure of dynactin complex at 6.3 angstrom resolution | |||||||||
Map data | CryoEM reconstruction of dynactin complex from pig brain at 6.3 angstrom resolution. | |||||||||
Sample |
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Keywords | dynactin / dynein co-factor / actin-like filament / cellular cargo transport | |||||||||
Biological species | Sus scrofa domesticus (domestic pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.3 Å | |||||||||
Authors | Zhang K / Urnavicius L / Diamant AG / Motz C / Schlager MA / Yu M / Patel NA / Robinson CV / Carter AP | |||||||||
Citation | Journal: Science / Year: 2015 Title: The structure of the dynactin complex and its interaction with dynein. Authors: Linas Urnavicius / Kai Zhang / Aristides G Diamant / Carina Motz / Max A Schlager / Minmin Yu / Nisha A Patel / Carol V Robinson / Andrew P Carter / Abstract: Dynactin is an essential cofactor for the microtubule motor cytoplasmic dynein-1. We report the structure of the 23-subunit dynactin complex by cryo-electron microscopy to 4.0 angstroms. Our ...Dynactin is an essential cofactor for the microtubule motor cytoplasmic dynein-1. We report the structure of the 23-subunit dynactin complex by cryo-electron microscopy to 4.0 angstroms. Our reconstruction reveals how dynactin is built around a filament containing eight copies of the actin-related protein Arp1 and one of β-actin. The filament is capped at each end by distinct protein complexes, and its length is defined by elongated peptides that emerge from the α-helical shoulder domain. A further 8.2 angstrom structure of the complex between dynein, dynactin, and the motility-inducing cargo adaptor Bicaudal-D2 shows how the translational symmetry of the dynein tail matches that of the dynactin filament. The Bicaudal-D2 coiled coil runs between dynein and dynactin to stabilize the mutually dependent interactions between all three components. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2854.map.gz | 11 MB | EMDB map data format | |
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Header (meta data) | emd-2854-v30.xml emd-2854.xml | 9.7 KB 9.7 KB | Display Display | EMDB header |
Images | image2854.png | 143 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2854 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2854 | HTTPS FTP |
-Related structure data
Related structure data | 2855C 2856C 2857C 2860C 2861C 2862C 5adxC 5afrC 5afuC C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2854.map.gz / Format: CCP4 / Size: 173.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM reconstruction of dynactin complex from pig brain at 6.3 angstrom resolution. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Dynactin complex from pig brain
Entire | Name: Dynactin complex from pig brainDynactin |
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Components |
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-Supramolecule #1000: Dynactin complex from pig brain
Supramolecule | Name: Dynactin complex from pig brain / type: sample / ID: 1000 Details: The sample was stored in -80 degrees Celcius freezer before being loaded onto the grid. Oligomeric state: One dynactin complex / Number unique components: 1 |
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Molecular weight | Experimental: 1.06 MDa / Theoretical: 1.06 MDa / Method: Mass spectrometry |
-Macromolecule #1: Arp1
Macromolecule | Name: Arp1 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Oligomeric state: Octamer / Recombinant expression: No |
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Source (natural) | Organism: Sus scrofa domesticus (domestic pig) / synonym: pig / Tissue: Brain / Location in cell: cytoplasm |
Molecular weight | Experimental: 43 KDa / Theoretical: 43 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.07 mg/mL |
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Buffer | pH: 6.5 Details: 50 mM KCl, 5 mM DDT, 0.1 mM Mg-ATP, 1 mM MgCl2 and 25 mM KH2PO4-K2HPO4 |
Grid | Details: R2/2 400-square-mesh copper grids with thin carbon support |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 105 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 7.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 47000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Temperature | Min: 80 K / Max: 100 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 96,000 times magnification |
Date | Apr 4, 2014 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 4483 / Average electron dose: 51 e/Å2 / Details: 51 frames per movie / Bits/pixel: 32 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each particle by Gctf |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 80865 |
Details | The particles were selected using the GPU accelerated automatic selection program Gautomatch. The CTF parameter were determined and refined using a GPU accelerated program Gctf |